Research workbench
Crystal structure of BAXP168G in complex with an activating antibody
Analyse Crystal structure of BAXP168G in complex with an activating antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W5X
- Type
- protein
- Length
- 591 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C10 Fab' light chain; 3C10 Fab' heavy chain; Apoptosis regulator bax
- UniProt
- Q07812
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | 3C10 Fab' light chain | protein | 212 | 6% helix, 51% strand | — |
| H | 3C10 Fab' heavy chain | protein | 212 | 11% helix, 55% strand | — |
| A | Apoptosis regulator bax | protein | 167 | 71% helix, 0% strand | Q07812 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.61 | 0.78 | 39 | empty |
| 2 | 212 | 0.43 | 0.72 | 37 | EDO |
| 3 | 109 | 0.42 | 0.77 | 19 | empty |
| 4 | 79 | 0.32 | 0.74 | 17 | empty |
| 5 | 68 | 0.30 | 0.74 | 15 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1600 Ų buried · 13 hydrogen bonds · protein-protein
- H–A · 630 Ų buried · 13 hydrogen bonds · protein-protein
- L–A · 242 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 5W5X · Crystal structure of BAXP168G in complex with an activating antibody · the same entry in another collection · chain L against L, TM-score 1.00
- Q07812 · AlphaFold monomer V2.0 prediction for apoptosis regulator bax (Q07812) · a predicted model of the same protein · chain A against A, TM-score 0.90
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q07812
- Elsewhere: RCSB PDB 5W5X · PDBe 5W5X · UniProt Q07812
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